Digestive tract Microbiome Analysis

The bacterial microbiome of digestive tract contributes substantial benefit to the host. It is critically important to compare the microbiome of healthy and disease persons in order to detect significant variations both in disease states and in pre-clinical conditions to understand disease onset and progression. In addition, the important role of digestive tract microbiota provides the rationale for reflect the relationship between obesity and digestive tract microbiome. Metagenomics combined with 16S rRNA gene sequence analyses was applied to uncover the complexity and functional diversity of the digestive tract microbiome.

Composition of the adult digestive tract bacterial microbiome

Fig.1 Composition of the adult digestive tract bacterial microbiome

Potential Research Directions of Digestive tract Microbiota Analysis

• Explore the differences in digestive tract composition and content between the healthy state and in a variety of disease states, such as atherosclerosis, type 2 diabetes, non-alcoholic fatty liver disease, obesity and inflammatory bowel disease.
• Explore the differences in digestive tract composition and content during the development of a certain disease to search for disease-related biomarkers
• Explore the differences in digestive tract composition and content at different developmental stages of the same individual
• Explore the differences in digestive tract composition and content at different body parts of the same individual

Technical Platforms

With our next-generation sequencing (NGS) technology, PacBio SMRT sequencing, and Nanopore sequencing platforms, we have the tool to identify, quantify and analysis the digestive tract microbiome. With this high-throughput technology we can perform complete metagenomics studies capable of surveying the genomes of entire communities, including those of unculturable organisms.

Illumina Hiseq Illumina Miseq Ion PGM PacBio SMRT system
Gut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome Analysis
Nanopore system PCR-DGGE Real-time qPCR Clone library
Gut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome Analysis

What Can Creative Biogene Do?

Creative Biogene offers extensive microbiome analysis portfolio includes not only consultancy, study design, sampling solutions and sequencing, but also downstream bioinformatic and biostatistical analyses. 

Project Workflow

High-throughput sequencing analysis process

Fig.2 High-throughput sequencing analysis process

High-throughput sequencing analysis process

Fig.3 PCR-DGGE analysis process

Service Specifications

Sample requirements and preparation

• Sample: Genomic DNA
• Quality requirements: ≥ 300 ng, ≥ 10 ng/μL, OD260/280=1.8-2.0, non-degradative
• Shipment: Dry ice or ice packs
• Repeated freeze-thaw cycles should be avoided

Detectable Microorganisms

• Bacteria
• Fungi
• Viruses

Basic analysis

• Sequence Filtering and Trimming
• Sequence Length Distribution
• OTU Clustering and Species Annotation
• Diversity Index
• Shannon-Wiener Curve
• Rank-Abundance Curve
• Rarefraction Curve
• Multiple Contrast
• Heatmap
• Principal Components Analysis (PCA)

Routine analysis

• Heatmap
• VENN
• Principal Components Analysis (PCA)
• Microbial Community Structure Analysis
• α Diversity Index Analysis
• Matastats Analysis
• Weighted Unifrac test
• CCA/RDA Analysis

Advanced data analysis

• Phylogenetic Tree
• LDA-Effect Size (LEfSe)
• Network Analysis
• Correlation Analysis

References
1. Lin, S.-W., Freedman, N. D., Shi, J., Gail, M. H., Vogtmann, E., Yu, G., … Abnet, C. C. (2015). Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index. Obesity, 23(4), 862–869.
2. Segata, N., Haake, S.K., Mannon, P. et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13, R42 (2012).

For research use only.

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